This subproject is one of many research subprojects utilizing the resources provided by a Center grant funded by NIH/NCRR. The subproject and investigator (PI) may have received primary funding from another NIH source, and thus could be represented in other CRISP entries. The institution listed is for the Center, which is not necessarily the institution for the investigator. We developed a new, mass spectrometry-based method for measuring affinity constants for specific metal ion binding to DNA, particularly to quadruplex DNA. This method, which is applicable to other systems, utilizes the gas-phase signals, as measured by mass spectrometry, from the bound and unbound species as input into a mathematical model that determines various parameters [unreadable]one of which is the binding affinity constant [unreadable]with a non-linear least squares fitting algorithm. The system used to develop and test the model was the thrombin-binding aptamer, an appropriate quadruplex structure that binds both K+ and Sr2+ cations.